added AppNameFilter to resolve app_name issue

cgatcore/pipeline/app_name_filter.py

@@ -0,0 +1,25 @@
+import logging
+
+class AppNameFilter(logging.Filter):
+    """Filter that adds an app_name attribute to log records."""
+
+    def __init__(self, app_name):
+        """Initialize the filter with an app name.
+        
+        Args:
+            app_name (str): Name to be added to log records
+        """
+        super().__init__()
+        self.app_name = app_name
+
+    def filter(self, record):
+        """Add app_name attribute to the record.
+        
+        Args:
+            record (LogRecord): The log record to filter
+            
+        Returns:
+            bool: Always returns True to allow the record through
+        """
+        record.app_name = self.app_name
+        return True

cgatcore/pipeline/control.py

@@ -507,33 +507,27 @@ def ruffus_return_dag(stream,
 
 
 def setup_logging(args, pipeline=None):
-
+    """setup logging.
+    """
     logger = logging.getLogger("cgatcore.pipeline")
 
     if args.log_config_filename is None:
-
-        # set up default file logger
-        handler = logging.FileHandler(
-            filename=args.pipeline_logfile,
-            mode="a")
-
-        if pipeline is not None:
-            pipeline_name = pipeline.name
+        if args.verbose:
+            level = logging.DEBUG
+        elif args.quiet:
+            level = logging.ERROR
         else:
-            pipeline_name = get_params().get("pipeline_name", "main")
-
-        handler.setFormatter(
-            E.MultiLineFormatter(
-                "%(asctime)s %(levelname)s "
-                "%(app_name)s %(module)s "
-                "- %(message)s"))
+            level = logging.INFO
 
-        logger.addFilter(LoggingFilterpipelineName(name=pipeline_name))
+        format = '# %(asctime)s %(app_name)s %(levelname)s %(message)s'
+        formatter = logging.Formatter(format)
+        handler = logging.StreamHandler(sys.stdout)
+        handler.setFormatter(formatter)
         logger.addHandler(handler)
+        logger.setLevel(level)
 
-        logger.info("pipeline log is {}".format(
-            args.pipeline_logfile))
-
+        if pipeline is not None:
+            logger.addFilter(LoggingFilterpipelineName(pipeline))
     return logger